Table 4.

(a) Gain and loss BCL6 targets comparison between ARACNe and hARACNe by shRNA library and (b) hypergeometric test in order to check if the gain is significantly derived from FPs.

(a)
BCL6: shRNA library		LY7			BCL6: shRNA library	Pfeiffer			BCL6: shRNA library	VAL
		TP	FP	Fisher's exact test p-value of inferred interactions		TP	FP	Fisher's exact test p-value of inferred interactions		TP	FP	Fisher's exact test p-value of inferred interactions
HG-U95Av2
DPI1		54	280	0.0136	DPI1	144	190	1.06×10−7	DPI1	117	217	6.97×10−5
DPI2		57	265	0.001614	DPI2	146	176	1.60×10−9	DPI2	118	204	6.32×10−6
DPI3		56	262	0.001988	DPI3	144	174	2.28×10−9	DPI3	117	201	5.54×10−6
DPI4		56	262	0.001988	DPI4	144	174	2.28×10−9	DPI4	117	201	5.54×10−6
gain		2	18	n.a.	gain	0	16	n.a.	gain	0	16	n.a.
(b)
HG-U95Av2	total gain between DPI1 and DPI4(nested)	LY7			total gain between DPI1 and DPI4(nested)	Pfeiffer			total gain between DPI1 and DPI4(nested)	VAL
		TP	FP	hypergeometric test p-value		TP	FP	hypergeometric test p-value		TP	FP	hypergeometric test p-value
	20	2	18	5.60×10−14	16	0	16	8.64×10−7	16	0	16	2.53×10−8